Is this a Y-adapter design? If so, the P7 and P5 need to anneal over the last 12 bases of the P5/first 12 bases of the P7, with a 3' "T" overhang to work with many Illumina work flows. When you add 8...

Did you see much phiX index hopping? Searching the "undetermined" fastq for index hops involving one of i7/i5 GGGGGGGG/TCGTAGTG I tentatively identified a fair number. Of course they may just be the...

You can buy the UDI 96 and/or the UDI 384 kit from IDT as a custom order. Just contact their sales. We bought the UDI 96. Made libraries (both no Amp DNA and RNAseq libraries) from them. Ran them on...

Actually you can purchase full (96 or 384) UDI adapter sets from IDT. Although last I checked they were still a custom synthesis order. Which means you get more adapter than you are likely to use at...

No reads, or no clusters?
Nextera sequencing primers aren't included in HiSeq High Output chemstry reagents. But they are in MiSeq/HiSeq Rapid chemsitry and so should be in the NextSeq reagent kits....